Starting phenix.real_space_refine on Sat Feb 17 16:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x98_22104/02_2024/6x98_22104.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 12078 2.51 5 N 3228 2.21 5 O 3828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19269 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "K" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 10.39, per 1000 atoms: 0.54 Number of scatterers: 19269 At special positions: 0 Unit cell: (157.59, 143.17, 118.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3828 8.00 N 3228 7.00 C 12078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.05 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Simple disulfide: pdb=" SG CYS K 35A" - pdb=" SG CYS K 50 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 156 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 133 " " NAG A 615 " - " ASN A 276 " " NAG A 616 " - " ASN A 339 " " NAG A 619 " - " ASN A 363 " " NAG A 620 " - " ASN A 332 " " NAG A 621 " - " ASN A 234 " " NAG A 622 " - " ASN A 392 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 156 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 133 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 339 " " NAG C 619 " - " ASN C 363 " " NAG C 620 " - " ASN C 332 " " NAG C 621 " - " ASN C 234 " " NAG C 622 " - " ASN C 392 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 295 " " NAG G 609 " - " ASN G 301 " " NAG G 610 " - " ASN G 156 " " NAG G 611 " - " ASN G 160 " " NAG G 612 " - " ASN G 133 " " NAG G 615 " - " ASN G 276 " " NAG G 616 " - " ASN G 339 " " NAG G 619 " - " ASN G 363 " " NAG G 620 " - " ASN G 332 " " NAG G 621 " - " ASN G 234 " " NAG G 622 " - " ASN G 392 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN C 88 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 262 " " NAG W 1 " - " ASN G 197 " " NAG X 1 " - " ASN G 386 " Time building additional restraints: 8.23 Conformation dependent library (CDL) restraints added in 3.4 seconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 20.8% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.633A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.763A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.244A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 474 through 479 Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.166A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR H 33 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.505A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP H 96 " --> pdb=" O ALA H 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA H 100E" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.950A pdb=" N TYR F 33 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP F 96 " --> pdb=" O ALA F 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 100E" --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 301 " --> pdb=" O ILE G 323A" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR K 33 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET K 35 " --> pdb=" O CYS K 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS K 50 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP K 96 " --> pdb=" O ALA K 100E" (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA K 100E" --> pdb=" O ASP K 96 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4334 1.32 - 1.45: 5735 1.45 - 1.58: 9392 1.58 - 1.72: 9 1.72 - 1.85: 180 Bond restraints: 19650 Sorted by residual: bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.426 0.071 1.40e-02 5.10e+03 2.54e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" N PRO G 470 " pdb=" CA PRO G 470 " ideal model delta sigma weight residual 1.465 1.414 0.052 1.19e-02 7.06e+03 1.88e+01 bond pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 1.465 1.414 0.051 1.19e-02 7.06e+03 1.87e+01 ... (remaining 19645 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.20: 300 104.20 - 111.71: 8952 111.71 - 119.21: 7672 119.21 - 126.71: 9499 126.71 - 134.21: 280 Bond angle restraints: 26703 Sorted by residual: angle pdb=" N LEU A 261 " pdb=" CA LEU A 261 " pdb=" C LEU A 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.57e+01 angle pdb=" N LEU C 261 " pdb=" CA LEU C 261 " pdb=" C LEU C 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.56e+01 angle pdb=" N LEU G 261 " pdb=" CA LEU G 261 " pdb=" C LEU G 261 " ideal model delta sigma weight residual 113.28 123.87 -10.59 1.22e+00 6.72e-01 7.53e+01 angle pdb=" C CYS G 239 " pdb=" N PRO G 240 " pdb=" CA PRO G 240 " ideal model delta sigma weight residual 119.56 127.82 -8.26 1.02e+00 9.61e-01 6.55e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.79 -8.23 1.02e+00 9.61e-01 6.51e+01 ... (remaining 26698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12114 21.85 - 43.71: 330 43.71 - 65.56: 75 65.56 - 87.41: 30 87.41 - 109.27: 18 Dihedral angle restraints: 12567 sinusoidal: 5793 harmonic: 6774 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.45 88.45 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.44 88.44 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.43 88.43 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 12564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2400 0.103 - 0.206: 719 0.206 - 0.308: 97 0.308 - 0.411: 0 0.411 - 0.514: 3 Chirality restraints: 3219 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.38e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.30e+01 ... (remaining 3216 not shown) Planarity restraints: 3351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 620 " -0.055 2.00e-02 2.50e+03 4.48e-02 2.50e+01 pdb=" C7 NAG A 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG A 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG A 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 620 " -0.055 2.00e-02 2.50e+03 4.47e-02 2.49e+01 pdb=" C7 NAG G 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG G 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG G 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 620 " 0.054 2.00e-02 2.50e+03 4.44e-02 2.46e+01 pdb=" C7 NAG C 620 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 620 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 620 " -0.071 2.00e-02 2.50e+03 pdb=" O7 NAG C 620 " -0.012 2.00e-02 2.50e+03 ... (remaining 3348 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7360 2.87 - 3.38: 16296 3.38 - 3.89: 32071 3.89 - 4.39: 36098 4.39 - 4.90: 60324 Nonbonded interactions: 152149 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" OG1 THR G 499 " model vdw 2.363 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.364 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.364 2.440 nonbonded pdb=" N ASN G 133 " pdb=" OD1 ASN G 133 " model vdw 2.368 2.520 nonbonded pdb=" N ASN A 133 " pdb=" OD1 ASN A 133 " model vdw 2.368 2.520 ... (remaining 152144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.990 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 52.800 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.126 19650 Z= 1.274 Angle : 1.711 11.300 26703 Z= 1.116 Chirality : 0.093 0.514 3219 Planarity : 0.009 0.045 3303 Dihedral : 11.484 109.268 8085 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2313 helix: 0.54 (0.26), residues: 354 sheet: 0.85 (0.19), residues: 708 loop : 0.98 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.009 TRP B 571 HIS 0.008 0.002 HIS C 374 PHE 0.027 0.006 PHE F 67 TYR 0.050 0.008 TYR A 40 ARG 0.007 0.001 ARG G 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 529 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6820 (p-80) cc_final: 0.6506 (m170) REVERT: C 72 HIS cc_start: 0.7000 (p-80) cc_final: 0.6443 (m170) REVERT: G 72 HIS cc_start: 0.6797 (p-80) cc_final: 0.6446 (m170) REVERT: G 95 MET cc_start: 0.9027 (ptm) cc_final: 0.8701 (ptm) REVERT: G 424 ILE cc_start: 0.9128 (mm) cc_final: 0.8866 (mm) REVERT: I 632 ASP cc_start: 0.8405 (t70) cc_final: 0.8135 (t0) outliers start: 3 outliers final: 3 residues processed: 532 average time/residue: 0.3273 time to fit residues: 257.8564 Evaluate side-chains 255 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN D 640 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN I 640 GLN ** I 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19650 Z= 0.239 Angle : 0.667 8.463 26703 Z= 0.362 Chirality : 0.047 0.159 3219 Planarity : 0.004 0.043 3303 Dihedral : 8.622 65.301 3897 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.15 % Allowed : 8.52 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2313 helix: 2.03 (0.28), residues: 336 sheet: 0.55 (0.18), residues: 735 loop : 0.64 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 479 HIS 0.004 0.001 HIS A 105 PHE 0.016 0.002 PHE A 383 TYR 0.025 0.002 TYR B 638 ARG 0.004 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 315 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6754 (p-80) cc_final: 0.6494 (m170) REVERT: A 95 MET cc_start: 0.8923 (ptm) cc_final: 0.8677 (ptm) REVERT: B 535 MET cc_start: 0.7862 (mtp) cc_final: 0.7618 (mtt) REVERT: B 617 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6621 (mtm180) REVERT: B 632 ASP cc_start: 0.8563 (t70) cc_final: 0.8256 (t0) REVERT: B 634 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7297 (mm-30) REVERT: C 72 HIS cc_start: 0.6869 (p-80) cc_final: 0.6347 (m170) REVERT: D 632 ASP cc_start: 0.8512 (t70) cc_final: 0.8160 (t0) REVERT: D 634 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 23 CYS cc_start: 0.6131 (t) cc_final: 0.5613 (t) REVERT: G 72 HIS cc_start: 0.6697 (p-80) cc_final: 0.6400 (m170) REVERT: G 95 MET cc_start: 0.8926 (ptm) cc_final: 0.8579 (ptm) REVERT: I 632 ASP cc_start: 0.8527 (t70) cc_final: 0.8233 (t0) REVERT: I 634 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7497 (mm-30) outliers start: 64 outliers final: 49 residues processed: 363 average time/residue: 0.2984 time to fit residues: 168.4665 Evaluate side-chains 294 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 244 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN ** I 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19650 Z= 0.415 Angle : 0.694 7.518 26703 Z= 0.371 Chirality : 0.048 0.154 3219 Planarity : 0.005 0.050 3303 Dihedral : 7.503 51.352 3897 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.84 % Allowed : 9.90 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2313 helix: 1.80 (0.29), residues: 357 sheet: 0.59 (0.19), residues: 678 loop : -0.01 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 69 HIS 0.009 0.002 HIS A 374 PHE 0.020 0.002 PHE C 383 TYR 0.021 0.002 TYR F 58 ARG 0.005 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 249 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6835 (p-80) cc_final: 0.6629 (m-70) REVERT: A 104 MET cc_start: 0.8598 (ttt) cc_final: 0.8192 (ttt) REVERT: B 634 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7570 (mm-30) REVERT: L 58 VAL cc_start: 0.7522 (m) cc_final: 0.7306 (m) REVERT: C 72 HIS cc_start: 0.6850 (p-80) cc_final: 0.6378 (m170) REVERT: D 617 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6306 (mtm180) REVERT: D 632 ASP cc_start: 0.8694 (t70) cc_final: 0.8323 (t0) REVERT: D 661 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7383 (mm) REVERT: E 63 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7650 (mtmm) REVERT: G 72 HIS cc_start: 0.6748 (p-80) cc_final: 0.6501 (m-70) REVERT: G 104 MET cc_start: 0.8645 (ttm) cc_final: 0.8282 (ttt) REVERT: I 632 ASP cc_start: 0.8656 (t70) cc_final: 0.8283 (t0) REVERT: I 634 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7561 (mm-30) REVERT: J 63 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7792 (mtpp) outliers start: 78 outliers final: 54 residues processed: 311 average time/residue: 0.3077 time to fit residues: 147.6524 Evaluate side-chains 278 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 658 GLN D 575 GLN E 37 GLN G 411 ASN I 658 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19650 Z= 0.169 Angle : 0.546 8.134 26703 Z= 0.289 Chirality : 0.043 0.150 3219 Planarity : 0.004 0.044 3303 Dihedral : 6.357 44.838 3897 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.10 % Allowed : 10.93 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.17), residues: 2313 helix: 2.02 (0.28), residues: 357 sheet: 0.63 (0.19), residues: 717 loop : -0.09 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 571 HIS 0.003 0.001 HIS G 105 PHE 0.015 0.001 PHE C 53 TYR 0.021 0.002 TYR I 638 ARG 0.004 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 256 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6866 (p-80) cc_final: 0.6613 (m-70) REVERT: A 104 MET cc_start: 0.8514 (ttt) cc_final: 0.8122 (ttt) REVERT: B 617 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7491 (mtm180) REVERT: L 63 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7611 (mtpp) REVERT: C 72 HIS cc_start: 0.6847 (p-80) cc_final: 0.6361 (m170) REVERT: C 95 MET cc_start: 0.8382 (ptm) cc_final: 0.8170 (ttp) REVERT: D 617 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6257 (mtm180) REVERT: D 632 ASP cc_start: 0.8638 (t70) cc_final: 0.8148 (t0) REVERT: D 661 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7140 (mm) REVERT: E 63 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7622 (mtmm) REVERT: G 72 HIS cc_start: 0.6707 (p-80) cc_final: 0.6459 (m-70) REVERT: G 104 MET cc_start: 0.8521 (ttm) cc_final: 0.8314 (ttt) REVERT: G 141 ASP cc_start: 0.7829 (t70) cc_final: 0.7613 (t0) REVERT: I 632 ASP cc_start: 0.8601 (t70) cc_final: 0.8318 (t0) REVERT: I 634 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7656 (mm-30) REVERT: J 63 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7850 (mtpp) outliers start: 63 outliers final: 45 residues processed: 304 average time/residue: 0.3005 time to fit residues: 141.0355 Evaluate side-chains 271 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 223 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 166 optimal weight: 0.0770 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19650 Z= 0.244 Angle : 0.560 9.436 26703 Z= 0.295 Chirality : 0.043 0.145 3219 Planarity : 0.004 0.045 3303 Dihedral : 5.985 41.953 3897 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.25 % Allowed : 12.21 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2313 helix: 1.82 (0.29), residues: 366 sheet: 0.58 (0.19), residues: 684 loop : -0.11 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 69 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.002 PHE C 383 TYR 0.029 0.002 TYR I 638 ARG 0.006 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 238 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6934 (p-80) cc_final: 0.6654 (m-70) REVERT: A 104 MET cc_start: 0.8595 (ttt) cc_final: 0.8213 (ttt) REVERT: B 617 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7445 (mtm180) REVERT: L 63 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7623 (mtpp) REVERT: C 72 HIS cc_start: 0.6966 (p-80) cc_final: 0.6412 (m170) REVERT: D 617 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6148 (mtm180) REVERT: D 632 ASP cc_start: 0.8629 (t70) cc_final: 0.8238 (t0) REVERT: D 655 LYS cc_start: 0.8361 (tptp) cc_final: 0.8055 (tptt) REVERT: D 661 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7116 (mm) REVERT: E 63 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7516 (mtpp) REVERT: G 46 LYS cc_start: 0.8287 (mmmt) cc_final: 0.8073 (mmtt) REVERT: G 72 HIS cc_start: 0.6756 (p-80) cc_final: 0.6489 (m-70) REVERT: G 104 MET cc_start: 0.8601 (ttm) cc_final: 0.8400 (ttt) REVERT: I 632 ASP cc_start: 0.8651 (t70) cc_final: 0.8257 (t0) REVERT: I 634 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7759 (mm-30) REVERT: J 63 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7844 (mtpp) REVERT: J 88 CYS cc_start: 0.6753 (p) cc_final: 0.6498 (p) outliers start: 66 outliers final: 50 residues processed: 286 average time/residue: 0.3123 time to fit residues: 137.8888 Evaluate side-chains 274 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 478 ASN C 411 ASN I 575 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19650 Z= 0.420 Angle : 0.663 10.064 26703 Z= 0.348 Chirality : 0.047 0.175 3219 Planarity : 0.005 0.047 3303 Dihedral : 6.285 41.368 3897 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.55 % Allowed : 12.95 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2313 helix: 1.36 (0.29), residues: 384 sheet: 0.50 (0.19), residues: 681 loop : -0.34 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 69 HIS 0.008 0.002 HIS A 374 PHE 0.019 0.002 PHE A 383 TYR 0.024 0.002 TYR J 30 ARG 0.007 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 237 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7007 (p-80) cc_final: 0.6717 (m-70) REVERT: C 72 HIS cc_start: 0.7104 (p-80) cc_final: 0.6593 (m170) REVERT: D 617 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6313 (mtm180) REVERT: D 632 ASP cc_start: 0.8746 (t70) cc_final: 0.8515 (t0) REVERT: D 661 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7384 (mm) REVERT: E 63 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7546 (mtpp) REVERT: G 72 HIS cc_start: 0.6969 (p-80) cc_final: 0.6667 (m-70) REVERT: G 95 MET cc_start: 0.8606 (ptm) cc_final: 0.8054 (ttp) REVERT: G 161 MET cc_start: 0.7743 (ttm) cc_final: 0.7312 (ttt) REVERT: I 632 ASP cc_start: 0.8698 (t70) cc_final: 0.8173 (t0) REVERT: I 634 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7714 (mm-30) REVERT: J 63 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7914 (mtpp) outliers start: 72 outliers final: 55 residues processed: 293 average time/residue: 0.3035 time to fit residues: 136.7806 Evaluate side-chains 275 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19650 Z= 0.176 Angle : 0.541 8.051 26703 Z= 0.286 Chirality : 0.043 0.142 3219 Planarity : 0.004 0.043 3303 Dihedral : 5.732 36.806 3897 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.15 % Allowed : 14.08 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2313 helix: 1.63 (0.29), residues: 384 sheet: 0.48 (0.19), residues: 687 loop : -0.26 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 571 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE A 53 TYR 0.019 0.001 TYR I 638 ARG 0.007 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6985 (p-80) cc_final: 0.6654 (m-70) REVERT: A 104 MET cc_start: 0.8598 (ttt) cc_final: 0.8206 (ttt) REVERT: B 617 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7569 (mtm180) REVERT: C 72 HIS cc_start: 0.7015 (p-80) cc_final: 0.6393 (m170) REVERT: C 104 MET cc_start: 0.8588 (ttt) cc_final: 0.8327 (ttt) REVERT: C 161 MET cc_start: 0.8066 (tpp) cc_final: 0.7740 (ttm) REVERT: D 617 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6285 (mtm180) REVERT: D 632 ASP cc_start: 0.8614 (t70) cc_final: 0.8255 (t0) REVERT: D 661 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7177 (mm) REVERT: E 63 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7454 (mtpp) REVERT: G 72 HIS cc_start: 0.6741 (p-80) cc_final: 0.6395 (m-70) REVERT: G 95 MET cc_start: 0.8466 (ptm) cc_final: 0.7991 (ttp) REVERT: G 161 MET cc_start: 0.7663 (ttm) cc_final: 0.7413 (ttm) REVERT: I 632 ASP cc_start: 0.8714 (t70) cc_final: 0.8295 (t0) REVERT: I 634 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7620 (mm-30) REVERT: I 657 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7500 (mt-10) REVERT: J 63 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7902 (mtpp) REVERT: K 31 ASP cc_start: 0.7551 (m-30) cc_final: 0.7294 (m-30) outliers start: 64 outliers final: 52 residues processed: 296 average time/residue: 0.3089 time to fit residues: 140.9758 Evaluate side-chains 279 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19650 Z= 0.350 Angle : 0.618 12.178 26703 Z= 0.324 Chirality : 0.045 0.166 3219 Planarity : 0.004 0.046 3303 Dihedral : 5.849 38.206 3897 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.55 % Allowed : 13.88 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2313 helix: 1.53 (0.29), residues: 384 sheet: 0.46 (0.19), residues: 675 loop : -0.39 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 69 HIS 0.007 0.002 HIS A 374 PHE 0.017 0.002 PHE C 383 TYR 0.021 0.002 TYR E 95D ARG 0.008 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 227 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7049 (p-80) cc_final: 0.6718 (m-70) REVERT: B 617 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7570 (mtm180) REVERT: C 72 HIS cc_start: 0.7176 (p-80) cc_final: 0.6631 (m170) REVERT: C 161 MET cc_start: 0.8110 (tpp) cc_final: 0.7756 (ttm) REVERT: D 617 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6263 (mtm180) REVERT: D 661 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (mm) REVERT: E 63 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7511 (mtpp) REVERT: G 72 HIS cc_start: 0.6902 (p-80) cc_final: 0.6632 (m-70) REVERT: G 95 MET cc_start: 0.8483 (ptm) cc_final: 0.7987 (ttp) REVERT: G 104 MET cc_start: 0.8662 (ttm) cc_final: 0.8436 (ttt) REVERT: G 161 MET cc_start: 0.7738 (ttm) cc_final: 0.7510 (ttm) REVERT: I 632 ASP cc_start: 0.8770 (t70) cc_final: 0.8247 (t0) REVERT: I 634 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7555 (mm-30) REVERT: I 657 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7550 (mt-10) REVERT: J 5 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8226 (p) REVERT: J 63 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7947 (mtpp) outliers start: 72 outliers final: 56 residues processed: 283 average time/residue: 0.3011 time to fit residues: 131.5535 Evaluate side-chains 279 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 219 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19650 Z= 0.168 Angle : 0.542 11.935 26703 Z= 0.285 Chirality : 0.042 0.164 3219 Planarity : 0.004 0.043 3303 Dihedral : 5.390 35.173 3895 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.76 % Allowed : 14.87 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2313 helix: 1.80 (0.29), residues: 384 sheet: 0.48 (0.19), residues: 687 loop : -0.30 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.003 0.001 HIS A 374 PHE 0.015 0.001 PHE G 53 TYR 0.020 0.001 TYR E 95D ARG 0.008 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7010 (p-80) cc_final: 0.6667 (m-70) REVERT: A 104 MET cc_start: 0.8561 (ttt) cc_final: 0.8196 (ttt) REVERT: B 617 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7565 (mtm180) REVERT: C 72 HIS cc_start: 0.7150 (p-80) cc_final: 0.6600 (m170) REVERT: C 104 MET cc_start: 0.8570 (ttt) cc_final: 0.8274 (ttt) REVERT: C 161 MET cc_start: 0.8066 (tpp) cc_final: 0.7773 (ttm) REVERT: G 72 HIS cc_start: 0.6916 (p-80) cc_final: 0.6590 (m-70) REVERT: G 95 MET cc_start: 0.8324 (ptm) cc_final: 0.7881 (ttp) REVERT: G 161 MET cc_start: 0.7640 (ttm) cc_final: 0.7392 (ttm) REVERT: I 632 ASP cc_start: 0.8718 (t70) cc_final: 0.8259 (t0) REVERT: I 634 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7699 (mm-30) REVERT: J 63 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7892 (mtpp) outliers start: 56 outliers final: 41 residues processed: 291 average time/residue: 0.3034 time to fit residues: 135.4646 Evaluate side-chains 278 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN L 6 GLN C 411 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19650 Z= 0.334 Angle : 0.622 12.387 26703 Z= 0.325 Chirality : 0.045 0.225 3219 Planarity : 0.004 0.047 3303 Dihedral : 5.620 37.271 3893 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.51 % Allowed : 15.31 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2313 helix: 1.79 (0.29), residues: 375 sheet: 0.68 (0.18), residues: 750 loop : -0.41 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 631 HIS 0.007 0.002 HIS A 374 PHE 0.017 0.002 PHE C 383 TYR 0.021 0.002 TYR J 30 ARG 0.009 0.001 ARG K 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7124 (p-80) cc_final: 0.6791 (m-70) REVERT: A 104 MET cc_start: 0.8618 (ttt) cc_final: 0.8221 (ttt) REVERT: C 72 HIS cc_start: 0.7215 (p-80) cc_final: 0.6800 (m170) REVERT: C 104 MET cc_start: 0.8647 (ttt) cc_final: 0.8320 (ttt) REVERT: C 161 MET cc_start: 0.8109 (tpp) cc_final: 0.7784 (ttm) REVERT: D 632 ASP cc_start: 0.8655 (t0) cc_final: 0.8314 (t0) REVERT: G 46 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8084 (mmtt) REVERT: G 72 HIS cc_start: 0.6877 (p-80) cc_final: 0.6584 (m-70) REVERT: G 95 MET cc_start: 0.8467 (ptm) cc_final: 0.7996 (ttp) REVERT: G 104 MET cc_start: 0.8651 (ttm) cc_final: 0.8427 (ttt) REVERT: G 161 MET cc_start: 0.7726 (ttm) cc_final: 0.7510 (ttm) REVERT: I 632 ASP cc_start: 0.8703 (t70) cc_final: 0.8071 (t0) REVERT: I 634 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7718 (mm-30) REVERT: J 63 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7912 (mtpp) outliers start: 51 outliers final: 47 residues processed: 276 average time/residue: 0.2963 time to fit residues: 126.5897 Evaluate side-chains 278 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 411 ASN C 478 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086802 restraints weight = 34731.271| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.59 r_work: 0.3057 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19650 Z= 0.261 Angle : 0.586 13.060 26703 Z= 0.307 Chirality : 0.043 0.194 3219 Planarity : 0.004 0.050 3303 Dihedral : 5.507 36.362 3893 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.66 % Allowed : 15.16 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2313 helix: 2.00 (0.30), residues: 357 sheet: 0.59 (0.18), residues: 750 loop : -0.41 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 571 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE C 383 TYR 0.018 0.002 TYR E 95D ARG 0.009 0.000 ARG K 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.36 seconds wall clock time: 72 minutes 12.52 seconds (4332.52 seconds total)